New method provides panoramic view of protein-RNA interactions in living cells | Newswire in different cell types With this platform we now have a way to address all these questions Traditional methods used molecules to extract protein RNA complexes from living tissue But often the molecule only extracted the RNA Other times the protein bound too weakly to survive the purification process which involved stripping the complex of unwanted debris To address the issue Darnell and his team used a trick from test tube biochemistry that molecularly cements these regulatory proteins to RNA at the moment they touch The technique when applied to high throughput sequencing is called high throughput sequencing cross linking immunoprecipitation or HITS CLIP for short Since the RNA and RNA binding protein are fused together the researchers can really beat up the extract and rigorously purify the protein without fear of losing the RNA At the end of the day they are left with the RNA sequence to which the protein was bound They can then take these sequences to Rockefeller s high throughput sequence facility and with the help of Research Support Specialist Scott Dewell overlay them onto the genome and see where they match What they get is a map of every position on every transcribed RNA where the RNA binding protein is binding When DNA is transcribed into RNA the primary transcript is divided into many blocks called exons which are separated by empty spaces In order to convert the transcript into some sort of message all the spaces need to be removed but if an exon is dropped a different version of that protein which could carry a very different message is created That s RNA splicing says first author Donny Licatalosi a postdoctoral associate in the lab It is what gives rise to this massive pool of diverse and complex tissues with a relatively

Original URL path: http://newswire.rockefeller.edu/2008/11/02/new-method-provides-panoramic-view-of-protein-rna-interactions-in-living-cells/ (2016-02-13)Open archived version from archive

HITS-CLIP | Newswire many genes we have as it does with how we process them Now Rockefeller University scientists offer for the first time a genome wide view from the first chromosome to the last of how differences in RNA can explain how a worm and a human can each have 25 000 genes yet be so different More Tags HITS CLIP RNA Robert B Darnell Search for Categories Science News Awards and

Structure shows how a key protein in gene activation is controlled | Newswire and precocious activation of their genes Bacteria use the σ protein to control when their genes are turned on and off When σ binds to DNA the adjacent gene is turned on when it s not bound that gene is turned off A crystal structure depicting σ28 the initiation factor from the bacteria Aquifex aeolicus bound to its inhibitor protein FlgM has previously shown that FlgM inhibits σ28 by packing together its DNA binding domains which interferes with σ28 s ability to recognize DNA FlgM also covers up the part of σ28 that interacts with the RNA polymerase needed for gene expression But Seth Darst head of the Laboratory of Molecular Biophysics and Margareta Sörenson a former graduate student thought that perhaps σ28 adopted the same structure even without FlgM as a way to regulate itself We found that free σ28 in solution favors the conformation where all the DNA binding domains are tightly packed together says Darst But unlike when it is bound to FlgM the part of the protein that interacts with the RNA polymerase is still accessible When σ28 binds to the RNA polymerase this causes a conformational change in the σ28 protein opening up its DNA

Original URL path: http://newswire.rockefeller.edu/2006/12/01/structure-shows-how-a-key-protein-in-gene-activation-is-controlled/ (2016-02-13)Open archived version from archive

Researchers discover molecular “switch” that tells body to store or burn fat | Newswire 1 gene in 1988 together with M Daniel Lane Ph D at Johns Hopkins University SCD 1 has since been found to be very important for the synthesis of oleate despite the fact that mammalian diets supply abundant dietary oleate says Ntambi professor of biochemistry and nutritional sciences at the University of Wisconsin at Madison The next question the researchers asked was to what extent does repression of SCD 1 contribute to leptin s actions They hypothesized that if suppression of SCD 1 is required for leptin action then a mouse lacking SCD 1 should mimic some of leptin s effects The researchers crossed leptin deficient ob ob mice with a mouse strain called asebia which carries mutations in the SCD 1 gene The fatty acids that SCD 1 synthesizes are also required for normal function of sebaceous glands so its absence leads to the absence of sebaceous glands hence the name asebia Sebaceous glands are embedded in the skin over most of the body and are more concentrated in the scalp face forehead and eyes In the absence of sebaceous glands mice have patchy abnormal skin and abnormal corneas The researchers found that similar to leptin treatment removing SCD 1 markedly reduces the weight of the obese mouse at 16 weeks of age weight was reduced by 29 percent in females and 34 percent in males The reduced weight of these animals could be accounted for by a dramatic increase in energy expenditure Indeed removing SCD 1 completely corrected the effects of leptin deficiency on energy expenditure The repression of SCD 1 accounts for a significant proportion perhaps even all of the effects of leptin on energy expenditure says Friedman SCD 1 may act like a switch to control fat storage When SCD 1 is up the switch is flipped in the direction of storing fat and when it s down the switch is flipped in the direction of burning fat These data establish that SCD 1 is an important biological modulator of lipid metabolism adds Ntambi Obese leptin deficient mice also have massively fatty livers which is corrected when the mice are given leptin The lack of SCD 1 in the mutant mice also caused their livers to be normal and not fatty Inhibiting SCD 1 could be of potential use for reducing weight and for reducing fat content in liver which is also an important clinical problem says Friedman Fatty liver clinically known as steatosis often develops in people who are obese who abuse alcohol or other drugs or who are diabetic The researchers caution however that completely eliminating SCD 1 could cause other medical and health problems as evidenced by the abnormalities of asebia mice Mice which completely lack the SCD 1 enzyme suffer from corneal dryness which can lead to corneal opacities as well as the condition known as scarring dermatitis Inhibition of SCD 1 could also increase tissue damaging free radicals a potential sequelae of increased oxidative metabolism A key question is whether a

Original URL path: http://newswire.rockefeller.edu/2002/07/10/researchers-discover-molecular-switch-that-tells-body-to-store-or-burn-fat/ (2016-02-13)Open archived version from archive

Application deadline for faculty search is next week | Newswire who are in the early stages of their scientific careers in particular individuals who have excellent scientific accomplishments in their graduate and postgraduate training and who will bring an innovative and rigorous research program to the university The successful candidates will join an outstanding group of scientific faculty committed to fostering a new generation of exceptional scientists and will receive generous support from the university community Rockefeller faculty members reflect a wide range of research areas spanning many scientific fields The university is well suited for individuals with broad interests and who can take advantage of and flourish in our non departmental interdisciplinary structure The u niversity consists of 75 independent laboratories that are headed by faculty members at the ranks of a ssistant p rofessor h ead of l aboratory a ssociate p rofessor h ead of l aboratory and p rofessor h ead of l aboratory a ssistant and a ssociate p rofessor h ead of l aboratory appointments are tenure track f ull p rofessors ar e tenured For more information go to http www rockefeller edu facultysearch Tags faculty search newswire rockefeller edu Contact Joseph Bonner 212 327 8998 Bruce McEwen awarded Goldman Rakic Prize Scientists

New molecule identified in DNA damage response | Newswire have identified the molecule SMARCAL1 as involved in cells elaborate system for recognizing and repairing DNA damage during cell division The protein is pictured above green in the presence of DNA blue as the chromosomes align along the mitotic spindle red Lisa Postow a postdoctoral fellow in Hironori Funabiki s Laboratory of Chromosome and Cell Biology used mass spectroscopy to identify SMARCAL1 as involved in this intricate quality control process Working with Brian T Chait s Laboratory of Mass Spectrometry and Gaseous Ion Chemistry Postow found the protein in a proteomics screen for molecules that were drawn to a dangerous DNA repair problem called a double strand break In both human cells and in cells from African clawed frog egg extract Postow found that at double strand breaks SMARCAL1 gathered with another molecule called RPA which is known to coat broken strands of DNA and protect them while damage is repaired SMARCAL1 had an added interest too A mutation in the gene that produces it is involved in a rare but lethal disease called Schimke immuno osseous dysplasia a disorder that causes wide ranging problems including kidney malfunction immunodeficiency and growth inhibition To Postow s surprise she found that removing SMARCAL1 had little effect on double strand break repair However it did facilitate a different aspect of the DNA damage response called replication fork stabilization a process that holds steady the junction between parental and daughter strands the replication fork when replication is stalled because a problem has been detected For a mutation that causes such wide ranging and severe physiological effects it is surprising that the protein has such a relatively small effect at the cellular level Postow says Postow s findings were largely corroborated by independent new research into SMARCAL1 which was published this fall in four back

Mechanism of mutant histone protein in childhood brain cancer revealed | Newswire Together with DNA histones comprise the gene packaging material called chromatin The mutation occurs on histone H3 and involves the remarkably specific substitution of one amino acid lysine for another methionine at a key position on the histone s tail silencing the associated gene Normally gene silencing arises when an enzyme called a methyltransferase containing a structural region called the SET domain attaches a methyl chemical group to the lysine at position 27 in the H3 tail This highly specific chemical reaction called methylation is disrupted by the replacement of the lysine with methionine which could result in gene mis regulation Lewis and his colleagues looked at human DIPG tumors that contained the lysine to methionine substitution and determined that mutated histone H3 comprised anywhere from 3 6 percent to 17 6 percent of total H3 in DIPG samples They also found a global reduction in the levels of methylation of normal H3 histones when small amounts of the mutant H3 were added to normal human cells I have often said Every amino acid in histones matters says Allis who is the Joy and Jack Fishman Professor These studies underscore just how true that may be The researchers went on to demonstrate that the reduction in methylation of normal H3 histones results from interference with activity of a methyltransferase called PRC2 by the mutant histone Methylation of normal H3 by PRC2 leads to repression of genes involved in cellular growth pathways Without methylation genes involved in these pathways likely become activated promoting the growth of tumors in DIPG Allis and Lewis received funding from the National Institutes of Health and the Starr Cancer Consortium Key collaborators in this work included Oren Becher at Duke University Medical Center and Tom Muir at Princeton University and their colleagues Our findings provide us

Starr Cancer Consortium | Newswire inhibiting enzymes and could lead to the development of pharmaceuticals that mimic the action of these mutant proteins More Tags C David Allis histones Starr Cancer Consortium February 1 2013 Awards and Honors David Allis awarded 1 million grant from Starr Cancer Consortium Allis leads one of five cancer research teams that are winners of 5 million in grant awards from The Starr Foundation s Sixth Starr Cancer Consortium Grant